It is because as RuwaydaAtH showed, it IS two words like cherry is two different words. One must learn to form and remember which two words correctly. Memorize them not as one word with a space but as two words naming a single object. I don't see it as confusing at all, but as beautiful.
Furthermore, if one were to say Yáʼátʼééh is confusing because why does it mean Hello and also Like because those are two completely different things?, then I would say this, that one must see deeper into the language because the words describe their objects and relations between them (cherry: deer food; tomato: red plant). How so in this case of Yáʼátʼééh? Well, it's descriptive of the words Hello and Like: You say hi to people you like. I heard someone in a group ask Why did you say hi to them?, We don't like them? Right? So Like and Hellow are VERY related. When you say Yáʼátʼééh it's not a thin, two-faced hello, but an act of friendship and blessing. Blessing? How? Yáʼátʼééh abini is Good Morning to you. Just starting with Yáʼátʼééh you have started with the first part of the blessing. It is tied intricately to liking, to friendship, to greeting with blessings. It is not a thin acknowledgement of your presence but is a relationship being expressed at a deep level in a single word. It is even deeper than I have explained. Consider this, that when you say you like a certain food, you end the sentence with yáʼátʼééh: Nímasii bił yáʼátʼééh he or she likes potatoes. Food gives life; we like it for that as well as its tastes; so does friendship. When a heart suffers loss of a loved one and is broken, it gives up even food. Yes we use 'like' in English but we don't bring it forward into our greetings to others; the Navajo do. It's beautiful.
So you can have two objects, deer and food, to describe a single third object, cherries; and you can have a single word, Yáʼátʼééh, describing two seemingly different but related words, Hello and Like. Very beautiful language and thought process.
All of what you've said is entirely correct. But it's also entirely unhelpful. Duolingo is supposed to teach languages. Your comment amounts to "Well to learn the language you need to learn the language." Given that this course has no guides, it's difficult for people to learn those nuances. Besides, even though it is two separate words, Duo should still show them together as meaning "tomato" because thats what the question is. That's what its like for other languages where a phrase is required to describe one thing. For example, "potato" in French is 3 words "pomme de terre". This literally means "apple of the ground". But all 3 are required to give the meaning 'potato'. So, if you click on the potato guide box, it shows you the 3 as a single phrase.